def test_p11():
'''
Test to plot a phase function, and make sure it is normalized properly
'''
alam = 500*u.nm
r = 10*u.micron
x = (2*math.pi * r / alam).to('1').value
num_theta = 1000
theta = hbt.frange(0,math.pi, num_theta)
p11 = np.zeros(num_theta)
phase = math.pi - theta # Theta is scattering angle
nm_refract = complex(1.5, 0.1)
mie = Mie(x=x, m=nm_refract) # This is only for one x value, not an ensemble
qext = mie.qext()
qsca = mie.qsca()
qbak = mie.qb()
for i,theta_i in enumerate(theta):
(S1, S2) = mie.S12(np.cos(theta_i)) # Looking at code, S12 returns tuple (S1, S2). S3, S4 are zero for sphere.
k = 2*pi / alam
sigma = pi * r**2 * qsca # For (S1,S2) -> P11: p. 2 of http://nit.colorado.edu/atoc5560/week8.pdf
# qsca = scattering efficiency. sigma = scattering cross-section
p11[i] = 4 * pi / (k**2 * sigma) * ( (np.abs(S1))**2 + (np.abs(S2))**2) / 2
# Check the normalization of the resulting phase function.
dtheta = theta[1] - theta[0]
norm = np.sum(p11 * np.sin(theta) * dtheta) # This should be 2, as per TPW04 eq. 4
print('Normalized integral = {:.2f}'.format(norm))
plt.plot(phase*hbt.r2d, p11)
plt.yscale('log')
plt.title('X = {:.1f}'.format(x))
plt.xlabel('Phase angle')
plt.ylabel('$P_{11}$')
plt.show()
p = plt.plot([0,10], [0,10])
currentAxis = plt.gca()
currentAxis.add_patch(Rectangle((0.5, 0.5), 0.7, 0.7,alpha=0.1, color='red'))
plt.text(1, 1, 'Danger')
plt.show()
def other():
theta_0 = 0
theta_1 = pi
num_theta = 100
theta = hbt.frange(theta_0, theta_1, num_theta)
dtheta = theta[1] - theta[0]
p11 = np.cos(theta) # lambertian phase function = cos(theta). This is the *surface* phase function --
# not the phase function for the entire sphere, which needs to be convolved with the
# crescent shape!
p11 = 1 # Integral = 2 for this value (isotropic scattering)
p11 = 8/(3 * pi) * (np.sin(theta) + (pi - theta) * np.cos(theta))
# Integral = 2 for this expression (disk-integrated scattering from lambert sphere)
# Madhusudhan & Burrows, 2012, http://arxiv.org/pdf/1112.4476v1.pdf, eq33
int = np.sum(p11 * np.sin(theta) * dtheta) # This integral should be 2, as per TE98 eq 16.
print("Total = {}".format(int))
t = pickle.load(lun)
lun.close()
groupmask = (t['Desc'] == 'Jupiter ring - search for embedded moons')
t_group = t[groupmask]
segment = 1 # 1, 2, or 3
fs = 15 # Set the font size
if (segment == 1): # 50 frames, upright
frames_med = np.array([1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19])
# frames_med = np.array([1,2,3,4,5])
num_frames_med = np.size(frames_med)
frames_data = hbt.frange(0,48,49) # 0 .. 49
if (segment == 2): # 5 frames, tilted sideways
frames_med = np.array([49,51,52,53,53])
num_frames_med = np.size(frames_med)
frames_data = frames_med
if (segment == 3): # 5 frames, tilted sideways
frames_med = hbt.frange(54,111,58)
num_frames_med = np.size(frames_med)
frames_data = frames_med
frame_arr = np.zeros((num_frames_med, 1024, 1024))
frame_sfit_arr = np.zeros((num_frames_med, 1024, 1024))
frame_ffit_arr = np.zeros((num_frames_med, 1024, 1024))
t['groupnum'] = np.zeros(len(t)).astype(int)
t['imagenum'] = np.zeros(len(t)).astype(int)
# Standardize the reqid field, so it is sortable
t['ReqID_fixed'] = t['ReqID']
for i in range(len(t)):
t['ReqID_fixed'][i] = fix_reqid(t['ReqID'][i])
# Loop over all the groups, and assign a group and image number to each file
for groupnum, group in enumerate(groups_all):
is_match = t['Desc'] == group
t['groupnum'][is_match] = groupnum
t['imagenum'][is_match] = hbt.frange(0,
np.sum(is_match) - 1).astype(int)
# Now get a list of all reqid's
reqids_all = astropy.table.unique(t, keys=(['ReqID_fixed']))['ReqID']
# Now get a list of reqid's, for rings only!
groups_rings = groups_all[5:]
groupmask = np.logical_or((t['Desc'] == groups_rings[0]),
(t['Desc'] == groups_rings[1]))
groupmask = np.logical_or(groupmask, t['Desc'] == groups_rings[2])
groupmask = np.logical_or(groupmask, t['Desc'] == groups_rings[3])
groupmask_rings = groupmask
t_rings = t[groupmask_rings]
index_group = 7 # Raw image, group
method = 'String' # Next, Previous, String, etc.
argument = '8-15' # 33, or 8/23, or 10-20, etc.
groupmask = (t['Desc'] == groups[index_group])
t_group = t[groupmask]
file = t_group[index_image]['Filename']
image = hbt.read_lorri(file)
image_proc = hbt.nh_jring_process_image(image, method, argument, index_group, index_image)
#stop
image_stray = hbt.nh_get_straylight_median(index_group, hbt.frange(8,15))
nx = np.shape(image)[0]
ny = np.shape(image)[1]
#image_stray = '/Users/throop/data/NH_Jring/out/straylight_median_g7_n8..15_sfit5,5.pkl'
xvals = range(nx)
yvals = range(ny)
(x,y) = np.meshgrid(xvals,yvals)
stretch = astropy.visualization.PercentileInterval(90) # PI(90) scales array to 5th .. 95th %ile.
image_s5 = hbt.remove_sfit(image,5)
plt.rcParams['figure.figsize'] = 5,5
plt.title('frame_ffit_med, n=' + repr(num_frames_med))
plt.show()
#stop
#####
#def f():
# nh_get_straylight_median(8,[50,51,52,52], do_sfit=True, power1=5, power2=5) # long movie, tilted portion
# nh_get_straylight_median(8,hbt.frange(0,49,50), do_sfit=True, power1=5, power2=5) # long movie, first 50 frames
#nh_get_straylight_median(5,hbt.frange(1,6,6), do_sfit=True, power1=5, power2=5) # best portrait, ansa
s = nh_get_straylight_median(6,hbt.frange(229,232), do_sfit=True, power1=5, power2=5) # 4x4 gossamer
a = hbt.read_lorri(35117774)
a = hbt.read_lorri(35120054)
a = a - hbt.sfit(a,5)
a = hbt.remove_brightest(a,0.99,symmetric=True) # Careful here -- don't crop the ring!
(s_norm,coeffs) = hbt.normalize_images(s,a)
plt.imshow(a - s_norm)
#plt.subplot(3,2,1) # Reversed! num cols, num rows ** Good reduction. Largest az etent.
#im = hbt.remove_brightest(image - frame_sfit_med, 0.97, symmetric=True)
#plt.imshow(hbt.remove_brightest(im - hbt.sfit(im,8), 0.97, symmetric=True), vmin=-20, vmax=20)
#plt.title('image - multi_median_sfit, sfit', fontsize=fs)
##plt.show()
#
#plt.subplot(3,2,2) # OK reduction. Bit lumpy though.
#im = hbt.remove_brightest(image - frame_ffit_med, 0.97, symmetric=True)
# self.is_flattened = False
lun = open(dir_out + file_pickle, 'rb')
t = pickle.load(lun) # Self.t is the *entire* table for all J-ring obs, not subset.
lun.close()
# Process the group names. Some of this is duplicated logic -- depends on how we want to use it.
groups = astropy.table.unique(t, keys=(['Desc']))['Desc']
stretch_percent = 90
stretch = astropy.visualization.PercentileInterval(stretch_percent) # PI(90) scales to 5th..95th %ile.
index_group = 5
index_images = hbt.frange(1,6)
# Extract the one group we are looking at
# NB: This creates an entirely new table -- *not* a view into the original table.
# If we modify values here, we need to explicitly write the changes back to the original.
groupmask = t['Desc'] == groups[index_group]
t_group = t[groupmask] #
num_images_group = np.size(t_group)
num_bins_radius = 300
num_bins_azimuth = 300
bins_radius = hbt.frange(126_000, 131_000, num_bins_radius)
bins_azimuth = hbt.frange(0, 2*math.pi, num_bins_azimuth)
t = pickle.load(lun)
lun.close()
groups = astropy.table.unique(t, keys=(['Desc']))['Desc']
groupmask = (t['Desc'] == groups[index_group])
t_group = t[groupmask]
####
# Read and plot the LHS image of a 1x3 mosaic of Gossamer ring images.
# This is a lot of lines of code, but most of it is just stacking images and scaling, which should be rewritten
# into a function.
index_group = 6
index_image = hbt.frange(181,184).astype(int) # Which frame from the group do we extract?
image_stray = hbt.nh_get_straylight_median(6, hbt.frange(185,188)) #
image_arr = np.zeros((1024, 1024, 4))
for i in range(4):
image = hbt.read_lorri(t_group[index_image[i]]['Filename'], autozoom=True)
image_arr[:,:,i] = image
image_sum = np.sum(image_arr,axis=2)
image_sum_sfit = hbt.remove_sfit(image_sum, 5)
(image_stray_scale,junk) = hbt.normalize_images(image_stray, image_sum_sfit)
final = image_sum_sfit - image_stray_scale
final = hbt.remove_brightest(final, 0.95, symmetric=True)
file_short = files[i].split('/')[-1]
if DO_INTERACTIVE:
k = input("File {}-{} ({} = {}): ".format(0, np.size(files)-1, i, file_short))
else:
k = repr(list_batch[ii]) # Load the next element, as a string
if (ii == np.size(list_batch)-1): # If we've hit the last element
DO_INTERACTIVE = True # And go back to interactive mode
if (k in ['x', 'q']): # QUIT
sys.exit(0)
if ('-' in k):
(i1, i2) = np.array(k.split('-')).astype('int')
list_batch = hbt.frange(int(i1), int(i2)).astype('int')
ii = 0 # Current element number, within our list
k = repr(list_batch[ii]) # Extract one element from it
print ("Running from {} to {}...".format(i1, i2))
DO_INTERACTIVE = False
if ('*' in k): # Wildcard search
searchstr = k.replace('*', '')
for ii,file in enumerate(files):
if (searchstr in file):
print("{}. {}".format(ii, file.split('/')[-1]))
if (k == 'l'): # List all files
for ii,file in enumerate(files):
print("{}. {}".format(ii, file.split('/')[-1]))
def nh_jring_process_image(image_raw,
method,
vars,
index_group=-1,
index_image=-1,
mask_sfit=None):
"""
Return image with stray light removed. Flux is preserved and no clipping is done.
Parameters
-----
image_raw:
NumPy array with the data image.
method:
Method of background subtraction, which can be 'Next', 'Prev', 'Polynomial', 'String', 'None',
'Grp Num Frac Pow', etc.
In general 'String' is the most flexible, and recommended.
It can be things like "5/0-10 r3 *2 mask_7_10':
- Make a median of Group 5, Images 0-10
- Rotate them all by 270 degrees
- Scale it to the data image
- Multiply background image by 2
- Subtract data - background
- Remove a 5th degree polynomial from the result [always done, regardless]
- Load the Photoshop-created mask file "mask_7_10" and incorporate via a tuple
- Return final result
vars:
The argument to the 'method'. Can be an exponent, a file number, a string, etc -- arbitrary, as needed.
index_group:
Index of current image. Not used except for Next/Prev.
index_image:
Index of current group. Not used except for Next/Prev.
mask_sfit:
An optional mask to be applied when doing the sfit. Ony pixels with True will be used.
This is to mask out satellites, stars, CRs, etc. so they don't affect the sfit().
"""
stretch_percent = 90
stretch = astropy.visualization.PercentileInterval(
stretch_percent) # PI(90) scales to 5th..95th %ile.
# Load the arrays with all of the filenames
dir_out = '/Users/throop/Data/NH_Jring/out/'
file_pickle = dir_out + 'nh_jring_read_params_571.pkl' # Filename to get filenames, etc.
lun = open(file_pickle, 'rb')
t = pickle.load(lun)
lun.close()
# Initialize variables
DO_MASK = False # We set this based on whether a mask is passed in or not
dir_mask_stray = dir_out.replace(
'out', 'masks') # Directory where the mask files are
# Process the group names. Some of this is duplicated logic -- depends on how we want to use it.
groups = astropy.table.unique(t, keys=(['Desc']))['Desc']
if (index_group != -1): # Only do this if we actually passed a group in
groupmask = (t['Desc'] == groups[index_group])
t_group = t[groupmask]
# Look up the filename, in case we need it.
file_image = t_group['Filename'][index_image]
if (method == 'Previous'):
file_prev = t_group['Filename'][index_image - 1]
# print "file = " + filename
print("file_prev = " + file_prev)
image_bg = hbt.read_lorri(file_prev, frac_clip=1.0, bg_method='None')
image_fg = image_raw
image = image_fg - image_bg
image_processed = image
if (method == 'Next'):
file_next = t_group['Filename'][index_image + 1]
image_bg = hbt.read_lorri(file_next,
frac_clip=1.0,
bg_method='None',
autozoom=True)
image_fg = image_raw
image = image_fg - image_bg
image_processed = image
if (method == 'Median'): # XXX not working yet
file_prev = t_group['Filename'][index_image - 1]
image_bg = hbt.read_lorri(file_prev, frac_clip=1.0, bg_method='None')
image_fg = image_raw
image = image_fg - image_bg
image_processed = image
if (method == 'Polynomial'):
power = vars
image = image_raw - hbt.sfit(
image_raw, power) # Look up the exponenent and apply it
image_processed = image
if (
method == 'Grp Num Frac Pow'
): # Specify to subtract a specified group#/image#, mult factor, and sfit power.
# I thought this would be useful, but it turns out we usually need to subtract
# a median of multiple images -- not just one -- so this is not very useful.
# Plus, the best power is usually 5, and the best frac can be calc'd
# with a linfit.
if (np.size(vars) == 0): # If no args passed, just plot the image
power = 0
frac = 0
image = image_raw
if (np.size(vars) == 1): # One variable: interpret as exponent
power = float(vars[0])
frac = 0
image = image_raw
image_bg = hbt.sfit(image, power, mask=mask_sfit)
image = image - image_bg
if (np.size(vars) == 2
): # Two variables: interpret as group num and file num
(grp, num) = vars
frac = 1
power = 0
if (
np.size(vars)
) == 3: # Three variables: interpret as group num, file num, fraction
(grp, num, frac) = vars
power = 0
if (np.size(vars) == 4
): # Four variables: Group num, File num, Fraction, Exponent
(grp, num, frac, power) = vars
if int(np.size(vars)) in [2, 3, 4]:
grp = int(grp)
num = int(num)
frac = float(frac)
power = int(power)
print("group={}, num={}, frac={}".format(grp, num, frac))
# print "Group = {}, num{}, Name = {}".format(name_group, num, name)
name_group = groups[grp]
groupmask = t['Desc'] == name_group
group_tmp = t[groupmask]
filename_bg = group_tmp['Filename'][num]
image_fg = image_raw
image_bg = hbt.read_lorri(filename_bg,
frac_clip=1,
bg_method='None')
image = image_fg - float(frac) * image_bg
image = image - hbt.sfit(image, power, mask=mask_sfit)
image_processed = image
# =============================================================================
# Do method 'None' (trivial)
# =============================================================================
if (method == 'None'):
image_processed = image = image_raw
#==============================================================================
# Do method 'String'. Complicated, but most useful.
#
# Parse a string like "6/112-6/129", or "129", or "6/114", or "124-129"
# or "6/123 - 129" or "6/123-129 r1 *0.5 p4 mask_7_12"
# or "".
#
# Except for the group and image number, the order of thse does not matter.
#==============================================================================
####
# As of 8-July-2017, this is the one I will generally use for most purposes.
#
# 'String' does this:
# o Subtract the bg image made by combining the named frames, and rotating and scaling as requested (optional)
# o Apply a mask file (optional)
# o Subtract a polynomial (optional). ** As of 17-Nov-2017, sfit is applied only to masked pixels, not full image.
#
####
if (method == 'String'):
str = vars
# =============================================================================
# Parse any rotation angle -- written as "r90" -- and remove from the string
# =============================================================================
angle_rotate_deg = 0
match = re.search('(r[0-9]+)', str)
if match:
angle_rotate_deg = int(match.group(0).replace(
'r', '')) # Extract the rotation angle
str = str.replace(match.group(0),
'') # Remove the whole phrase from string
if (
np.abs(angle_rotate_deg)
) <= 10: # Allow value to be passed as (1,2,3) or (90, 180, 270)
angle_rotate_deg *= 90
# Determine how much the bg frame should be scaled, to match the data frame. This is just a multiplicative
# factor that very crudely accomodates for differences in phase angle, exptime, etc.
# =============================================================================
# Parse any stray multiplication factor -- written as "*3" -- and remove from the string
# Multiplicative factor is used to scale the stray light image to be removed, up and down (e.g., up by 3x)
# =============================================================================
factor_stray_default = 1 # Define the default multiplicative factor
factor_stray = factor_stray_default
match = re.search(
'(\*[0-9.]+)', str
) # Match *3 *0.4 etc [where '*' is literal, not wildcard]
if match:
factor_stray = float(match.group(0).replace(
'*', '')) # Extract the multiplicative factor
str = str.replace(match.group(0),
'').strip() # Remove phrase from the string
# =============================================================================
# Parse any mask file -- written as "mask_7_0" -- and remove from the string
# =============================================================================
#
# This mask is a fixed pattern, read from a file, for stray light etc.
# It is *not* for stars or satellites, which are calculated separately.
#
# To make these mask files, the steps are...
# Maskfile is using same name structure as for the summed bg straylight images -- e.g., 8/0-48.
#
# True = good pixel. False = bad.
file_mask_stray = None
match = re.search('(mask[0-9a-z._\-]+)', str)
print("Str = {}, dir_mask_stray = {}".format(str, dir_mask_stray))
if match:
file_mask_stray = dir_mask_stray + match.group(
0) + '.png' # Create the filename
DO_MASK = True
str = str.replace(match.group(0),
'').strip() # Remove the phrase from the string
# =============================================================================
# Parse any polynomial exponent -- written as 'p5'
# This is the polynomial removed *after* subtracting Image - Stray
# =============================================================================
poly_after_default = 0 # Define the default polynomial to subtract.
# I could do 5, or I could do 0.
poly_after = poly_after_default
match = re.search('(p[0-9]+)', str)
if match:
poly_after = int(match.group(0).replace(
'p', '')) # Extract the polynomal exponent
str = str.replace(match.group(0),
'').strip() # Remove the phrase from the string
# =============================================================================
# Now parse the rest of the string
# =============================================================================
# The only part that is left is 0, 1, or 2 integers, which specify the stray light file to extract
# They must be in the form "7/12-15", or "7/12" or "12"
str2 = str.replace('-', ' ').replace('/', ' ').replace(
'None', '') # Get rid of any punctuation
vars = np.array(
str2.split(), dtype=int
) # With no arguments, split() breaks at any set of >0 whitespace chars.
# =============================================================================
# Now load the appropriate stray light image, based on the number of arguments passed
# =============================================================================
do_sfit_stray = False # Flag: When constructing the straylight median file, do we subtract polynomial, or not?
#
# Usually we want False. ie, want to do:
# out = remove_sfit(raw - stray)
# not
# out = remove_sfit(raw) - remove_sfit(stray)
if (np.size(vars) == 0): # "<no arguments>"
image = image_raw
image_processed = image
image_stray = 0 * image
if (np.size(vars) == 1): # "12" -- image number
image_stray = hbt.nh_get_straylight_median(
index_group, [int(vars[0])],
do_sfit=do_sfit_stray) # "122" -- assume current group
if (np.size(vars) == 2): # "7-12" -- image range
image_stray = hbt.nh_get_straylight_median(
index_group,
hbt.frange(int(vars[0]), int(vars[1])).astype('int'),
do_sfit=do_sfit_stray) # "122-129"
# -- assume current group
if (np.size(vars) == 3): # "7/12-20" -- group, plus image range
image_stray = hbt.nh_get_straylight_median(
int(vars[0]),
hbt.frange(vars[1], vars[2]).astype('int'),
do_sfit=do_sfit_stray) # "5/122 - 129"
if (np.size(vars) == 4
): # "7/12 - 7/20" (very wordy -- don't use this)
image_stray = hbt.nh_get_straylight_median(
int(vars[0]),
hbt.frange(vars[1], vars[3]).astype('int'),
do_sfit=do_sfit_stray) # "6/122 - 6/129"
# Adjust the stray image to be same size as original.
# Sometimes we'll have a 4x4 we want to use as stray model for 1x1 image -- this allows that.
# When we resize it, also adjust the flux (e.g., by factor of 16).
dx_stray = hbt.sizex(image_stray)
dx_im = hbt.sizex(image_raw)
ratio = dx_im / dx_stray
if (dx_stray < dx_im):
image_stray = scipy.ndimage.zoom(image_stray, ratio) / (
ratio**2) # Enlarge the stray image
if (dx_stray > dx_im):
image_stray = scipy.ndimage.zoom(image_stray, ratio) / (
ratio**2) # Shrink the stray image
#=============================================================================
# Now that we have parsed the string, do the image processing
#=============================================================================
# Load the Photoshop stray mask file, if it exists. Otherwise, make a blank mask of True.
if file_mask_stray:
try:
mask_stray = imread(
file_mask_stray
) > 128 # Read file. Mask PNG file is 0-255. Convert to boolean.
print("Reading mask file {}".format(file_mask_stray))
if (
len(np.shape(mask_stray)) > 2
): # If Photoshop saved multiple planes, then just take first
mask_stray = mask_stray[:, :, 0]
except IOError: # If mask file is missing
print("Stray light mask file {} not found".format(
file_mask_stray))
else:
mask_stray = np.ones(np.shape(image_raw), dtype=bool)
# Load the object mask. This masks out stars and satellites, which should not have sfit applied to them.
file_objects = os.path.basename(file_image).replace(
'.fit', '_objects.txt')
mask_objects = nh_jring_mask_from_objectlist(file_objects)
mask_objects = np.logical_not(
mask_objects) # Make so True = good pixel
# Merge the two masks together
mask = np.logical_and(
mask_objects, mask_stray) # Output good if inputs are both good
# Rotate the stray light image, if that has been requested
# [this probably doesn't work, but that's fine -- I didn't end up using this.]
image_stray = np.rot90(
image_stray, angle_rotate_deg /
90) # np.rot90() takes 1, 2, 3, 4 = 90, 180, 270, 360.
# Subract the final background image from the data image
image_processed = image_raw - factor_stray * image_stray
# print("Removing bg. factor = {}, angle = {}".format(factor_stray, angle_rotate_deg))
# Apply the mask: convert any False pixels to NaN in prep for the sfit
image_masked = image_processed.copy()
image_masked[mask == False] = math.nan
frac_good = np.sum(mask) / (np.prod(np.shape(mask)))
print("Applying mask, fraction good = {}".format(frac_good))
# Remove a polynomial from the result. This is where the mask comes into play.
# XXX NB: I think the logic here could be cleaned up. sfit() now allows a mask= argument ,
# but it must not have when I wrote this code.
sfit_masked = hbt.sfit(image_masked, poly_after)
image_processed = image_processed - sfit_masked
print("Removing sfit {}".format(poly_after))
# Plot the masks and sfits, for diagnostics
do_plot_masks = False
if do_plot_masks:
plt.subplot(1, 3, 1)
plt.imshow(stretch(mask))
plt.title('mask')
plt.subplot(1, 3, 2)
plt.imshow(stretch(image_masked))
plt.title('image_masked')
plt.subplot(1, 3, 3)
plt.imshow(sfit_masked)
plt.title('sfit_masked')
plt.show()
# =============================================================================
# END OF CASE STATEMENT FOR METHODS
# =============================================================================
# Remove a small bias offset between odd and even rows ('jailbars')
# This might be better done before the sfit(), but in reality probably doesn't make a difference.
image_processed = hbt.lorri_destripe(image_processed)
# If requested: plot the image, and the background that I remove.
# Plot to Python console, not the GUI.
# Test stretching here
# We use astropy's stretching here, rather than matplotlib's norm= keyword. The basic idea of both of these
# is the same, but I know that astropy has a percentile stretch available.
DO_DIAGNOSTIC = False
if (DO_DIAGNOSTIC):
stretch = astropy.visualization.PercentileInterval(
90) # PI(90) scales array to 5th .. 95th %ile
plt.rcParams['figure.figsize'] = 16, 6
# Column 1: raw image
im = image_raw
im = hbt.remove_sfit(im, degree=5)
plt.subplot(1, 3, 1) # vertical, horizontal, index
plt.imshow(stretch(hbt.remove_sfit(im, degree=5)))
plt.title('remove_sfit(image_raw, degree=5), mean=' +
hbt.trunc(np.mean(im), 3))
plt.colorbar()
# Column 2: Stray only. This will throw an error if we haven't read in a stray light file -- just ignore it.
plt.subplot(1, 3, 2)
try:
plt.imshow(stretch(hbt.remove_sfit(
image_stray,
degree=5))) # This won't do much since it is already applied
except UnboundLocalError:
print("No stray light to subtract")
plt.title('remove_sfit(stray_norm, degree=5), mean=' +
hbt.trunc(np.mean(im), 3))
# Column 3: raw - stray
plt.subplot(1, 3, 3)
try:
im = hbt.remove_sfit(image_raw - image_stray, degree=5)
plt.imshow(stretch(im))
except UnboundLocalError:
print("No stray light to subtract")
plt.title('remove_sfit(image_raw - image_stray, degree=5), med ' +
hbt.trunc(np.median(im), 3))
plt.show()
# Now return the array. If we have a mask, then we return it too, as a tuple
if (DO_MASK): # If we loaded a mask
return (image_processed, mask)
else:
return image_processed
dir_out = '/Users/throop/data/NH_Jring/out/' # Directory for saving of parameters, backplanes, etc.
dir_masks = dir_out.replace('out', 'masks')
lun = open(dir_out + file_pickle, 'rb')
t = pickle.load(lun)
lun.close()
# Process the group names. Some of this is duplicated logic -- depends on how we want to use it.
groups = astropy.table.unique(t, keys=(['Desc']))['Desc']
stretch_percent = 90
stretch = astropy.visualization.PercentileInterval(stretch_percent) # PI(90) scales to 5th..95th %ile.
index_imagesets = [hbt.frange(0,7), # First set: take all images 7/0 .. 7/7. Sum them.
hbt.frange(8,15),
hbt.frange(16,23),
hbt.frange(24,31),
hbt.frange(32,35),
hbt.frange(36,39),
hbt.frange(40,42),
hbt.frange(52,57),
hbt.frange(61,63),
hbt.frange(91,93),
hbt.frange(94,96)
]
index_imagesets = [hbt.frange(58,60)]
index_group = 7
def __init__(self, master, size_window):
self.master = master # This is the handle to the main Tk widget. I have to use it occasionally to
# set up event handlers, so grab it and save it.
self.size_window = size_window # Save the size of the whole Tk window, in pixels.
# Open the image stack
# self.stretch_percent = 90
# self.stretch = astropy.visualization.PercentileInterval(self.stretch_percent) # PI(90) scales to 5th..95th %ile.
#
name_ort = 'ORT4'
# name_ort = 'ORT2_OPNAV'
if (name_ort == 'ORT1'):
self.reqids_haz = ['K1LR_HAZ00', 'K1LR_HAZ01', 'K1LR_HAZ02', 'K1LR_HAZ03', 'K1LR_HAZ04']
# self.reqids_haz = ['K1LR_HAZ03', 'K1LR_HAZ01', 'K1LR_HAZ02']
self.reqid_field = 'K1LR_MU69ApprField_115d_L2_2017264'
self.dir_data = '/Users/throop/Data/ORT1/throop/backplaned/'
if (name_ort == 'ORT2'):
self.reqids_haz = ['K1LR_HAZ00', 'K1LR_HAZ01', 'K1LR_HAZ02', 'K1LR_HAZ03', 'K1LR_HAZ04']
# self.reqids_haz = ['K1LR_HAZ03', 'K1LR_HAZ01', 'K1LR_HAZ02']
self.reqid_field = 'K1LR_MU69ApprField_115d_L2_2017264'
self.dir_data = '/Users/throop/Data/ORT2/throop/backplaned/'
if (name_ort == 'ORT3'):
self.reqids_haz = ['K1LR_HAZ00', 'K1LR_HAZ01', 'K1LR_HAZ02', 'K1LR_HAZ03', 'K1LR_HAZ04']
self.reqid_field = 'K1LR_MU69ApprField_115d_L2_2017264'
self.dir_data = '/Users/throop/Data/ORT3/throop/backplaned/'
if (name_ort == 'ORT4'):
self.reqids_haz = ['K1LR_HAZ00', 'K1LR_HAZ01', 'K1LR_HAZ02', 'K1LR_HAZ03']
self.reqid_field = 'K1LR_MU69ApprField_115d_L2_2017264'
self.dir_data = '/Users/throop/Data/ORT4/throop/backplaned/'
if (name_ort == 'ORT2_OPNAV'):
self.dir_data = '/Users/throop/Data/ORT2/throop/backplaned/'
dirs = glob.glob(self.dir_data + '/*LR_OPNAV*') # Manually construct a list of all the OPNAV dirs
self.reqids_haz = []
for dir_i in dirs:
self.reqids_haz.append(os.path.basename(dir_i))
self.reqids_haz = sorted(self.reqids_haz)
self.reqid_field = 'K1LR_MU69ApprField_115d_L2_2017264'
# Set the edge padding large enough s.t. all output stacks will be the same size.
# This value is easy to compute: loop over all stacks, and take max of stack.calc_padding()[0]
self.padding = 61 # Amount to pad the images by. This is the same as the max drift btwn all images in stacks
self.zoom = 4 # Sub-pixel zoom to apply when shifting images. 1 for testing; 4 for production.
self.num_image = 0 # Which stack number to start on.
self.zoom_screen = 1 # 'Screen zoom' amount to apply. This can be changed interactively.
self.is_blink = False # Blinking mode is turned off by default
self.dt_blink = 300 # Blink time in ms
# Start up SPICE if needed
if (sp.ktotal('ALL') == 0):
sp.furnsh('kernels_kem_prime.tm')
# Set the RA/Dec of MU69. We could look this up from SPICE but it changes slowly, so just keep it fixed for now.
self.radec_mu69 = (4.794979838984583, -0.3641418801015417)
# Set the CA time. Roughly doing this is fine.
self.et_ca = sp.utc2et('2019 1 Jan 05:33:00')
# Boolean. For the current image, do we subtract the field frame, or not?
self.do_subtract = True
hbt.set_fontsize(20)
# Set the stretch range, for imshow. These values are mapped to black and white, respectively.
self.vmin_diff = -1 # Range for subtracted images
self.vmax_diff = 2
self.vmin_raw = -1 # Range for raw images (non-subtracted)
self.vmax_raw = 1000
# Restore the stacks directly from archived pickle file, if it exists
self.file_save = os.path.join(self.dir_data,
f'stacks_blink_{name_ort}_n{len(self.reqids_haz)}_z{self.zoom}.pkl')
if os.path.isfile(self.file_save):
self.restore()
else:
# If no pickle file, load the stacks from raw images and re-align them
# Load and stack the field images
print("Stacking field images")
self.stack_field = image_stack(os.path.join(self.dir_data, self.reqid_field)) # The individual stack
self.stack_field.align(method = 'wcs', center = self.radec_mu69)
(self.img_field, self.wcs_field) =\
self.stack_field.flatten(zoom=self.zoom, padding=self.padding) # Save the stacked image and WCS
# Load and stack the Hazard images
self.img_haz = {} # Output dictionary for the stacked images
self.stack_haz = {} # Output dictionary for the stacks themselves
self.wcs_haz = {} # Output dictionary for WCS for the stacks
for reqid in self.reqids_haz:
self.stack_haz[reqid] = image_stack(os.path.join(self.dir_data, reqid)) # The individual stack
self.stack_haz[reqid].align(method = 'wcs', center = self.radec_mu69)
(self.img_haz[reqid], self.wcs_haz[reqid]) =\
self.stack_haz[reqid].flatten(zoom=self.zoom, padding=self.padding)
# Put them in a dictionary
# Save the stacks to a pickle file, if requested
yn = input("Save stacks to a pickle file? ")
if ('y' in yn):
self.save()
# Set the sizes of the plots -- e.g., (15,15) = large square
figsize_image = (15,15)
self.fig1 = Figure(figsize = figsize_image) # <- this is in dx, dy... which is opposite from array order!
self.ax1 = self.fig1.add_subplot(1,1,1,
label = 'Image') # Return the axes
plt.set_cmap('Greys_r')
self.canvas1 = FigureCanvasTkAgg(self.fig1,master=master)
self.canvas1.show()
# Put objects into appropriate grid positions
self.canvas1.get_tk_widget().grid(row=1, column=1, rowspan = 1)
# Define some keyboard shortcuts for the GUI
# These functions must be defined as event handlers, meaning they take two arguments (self and event), not just one.
master.bind('q', self.quit_e)
master.bind('<space>', self.toggle_subtract_e)
master.bind('=', self.prev_e)
master.bind('-', self.next_e)
master.bind('h', self.help_e)
master.bind('?', self.help_e)
master.bind('<Left>', self.prev_e)
master.bind('<Right>', self.next_e)
master.bind('s', self.stretch_e)
master.bind('b', self.blink_e)
master.bind('t', self.blink_set_time_e)
master.bind('#', self.blink_set_sequence_e)
master.bind('z', self.zoom_screen_up_e)
master.bind('Z', self.zoom_screen_down_e)
master.bind('x', self.clear_current_objects_e)
master.bind('X', self.clear_all_objects_e)
master.bind('=', self.scale_max_up_e)
master.bind('+', self.scale_max_down_e)
master.bind('-', self.scale_min_up_e)
master.bind('_', self.scale_min_down_e)
master.bind('S', self.save_output_e)
self.canvas1.get_tk_widget().bind("<Button 1>", self.click_e)
# Set the initial image index
self.reqid_haz = self.reqids_haz[self.num_image] # Set it to 'K1LR_HAZ00', for instance.
# Initialize the list of found objects for each stack
# There is a list of objects for each individual stack (ie, for each frame in the blink)
self.list_objects = {}
for reqid_i in self.reqids_haz:
self.list_objects[reqid_i] = [] # Each entry here will be something like [(x, y, dn), (x, y, dn)]
# Initialize a set of matplotlib 'line' objects for the image.
# These correspond to the 'objects' above, which are really just points
self.list_lines = {}
for reqid_i in self.reqids_haz:
self.list_lines[reqid_i] = [] # Each entry here will be a list of plot objects, of type 'line'
# Set a list of frame numbers to animate. For default, do them all.
self.list_index_blink = hbt.frange(0, len(self.reqids_haz)-1) # List of indices ( [1, 2, 3] )
self.list_index_blink_str = ' '.join(np.array(self.list_index_blink).astype(str)) # Make into string ('1 2 3')
self.index_blink = 0 # where in the list of indices do we start? Current index.
# Plot the image
self.plot()
import hbt
sp.furnsh('kernels_kem_ats.tm')
utc_start = "2019 1 Jan 06:40:00"
utc_end = "2019 1 Jan 07:20:00"
et_start = sp.utc2et(utc_start)
et_end = sp.utc2et(utc_end)
et_mid = (et_start + et_end)/2
num_dt = 500
et = hbt.frange(et_start, et_end, num_dt)
name_target = 'MU69'
name_observer = 'New Horizons'
dist = np.zeros(num_dt)
phase = np.zeros(num_dt)
for i,et_i in enumerate(et):
(state,_) = sp.spkezr(name_target, et_i, 'J2000', 'LT+S', name_observer)
dist[i] = np.sqrt(np.sum(state[0:3]**2))
plt.plot(et - et_mid, dist)
plt.xlabel('Dist [km]')
plt.ylabel('Seconds from c/a')
plt.show()
def nh_ort1_find_rings():
plt.set_cmap('Greys_r')
stretch_percent = 90
stretch = astropy.visualization.PercentileInterval(stretch_percent) # PI(90) scales to 5th..95th %ile.
dir = '/Users/throop/Data/ORT1/throop/backplaned'
files = glob.glob(os.path.join(dir, '*', '*fits'))
hbt.figsize((15,8))
# Set up output arrays
ra_arr = []
dec_arr = []
reqid_arr = []
exptime_arr= []
et_arr = []
utc_arr = []
# Start up SPICE
if (sp.ktotal('ALL') == 0):
sp.furnsh('kernels_kem.tm')
for ii,file in enumerate(files):
hdu = fits.open(file)
print('Reading {}/{}: {}'.format(ii, len(files), os.path.basename(file)))
img = hdu[0].data
header = hdu[0].header
ra_arr.append(header['CRVAL1'])
dec_arr.append(header['CRVAL2'])
exptime_arr.append(header['EXPTIME'])
reqid_arr.append(header['REQID'])
et_arr.append(header['SPCSCET'])
utc_arr.append(sp.et2utc(header['SPCSCET'], 'C', 0))
radius_eq = hdu['RADIUS_EQ'].data
dradius = 1000
num_bins_radius = 100
bins_radius = hbt.frange(0, np.amax(radius), num_bins_radius)
dn_median_arr = np.zeros(num_bins_radius)
dn_mean_arr = np.zeros(num_bins_radius)
for i in range(num_bins_radius-1):
is_good = np.logical_and(radius_eq > bins_radius[i], radius_eq < bins_radius[i+1])
dn_median_arr[i] = np.nanmedian(img[is_good])
dn_mean_arr[i] = np.nanmean(img[is_good])
do_plot = False
if do_plot:
plt.subplot(1,2,1)
plt.plot(bins_radius, dn_median_arr, label = 'median')
plt.plot(bins_radius, dn_mean_arr, label = 'mean')
plt.legend(loc = 'upper right')
plt.title("{}/{} {}".format(ii,len(files), os.path.basename(file)))
plt.subplot(1,2,2)
plt.imshow(stretch(img))
plt.show()
hdu.close()
# =============================================================================
# Read the values into NumPy arrays
# =============================================================================
ra = np.array(ra_arr)
dec = np.array(dec_arr)
reqid = np.array(reqid_arr)
et = np.array(et_arr)
exptime = np.array(exptime_arr)
utc = np.array(utc_arr)
plt.plot(ra, dec, ls='none', marker = 'o', ms=2)
# Put them all into a table
t = Table( [ra, dec, et, utc, exptime, reqid],
names = ('RA', 'Dec', 'ET', 'UTC', 'EXPTIME', 'ReqID'))
t = Table([a, b, c], names=('a', 'b', 'c'), meta={'name': 'first table'})
w_haz0 = (t['ReqID'] == 'K1LR_HAZ00')
w_haz1 = (t['ReqID'] == 'K1LR_HAZ01')
w_haz2 = (t['ReqID'] == 'K1LR_HAZ02')
w_haz3 = (t['ReqID'] == 'K1LR_HAZ03')
w_haz4 = (t['ReqID'] == 'K1LR_HAZ04')
plt.plot(ra[w_haz0], dec[w_haz0], marker='o', ls='none')
plt.plot(ra[w_haz1], dec[w_haz1], marker='o', ls='none')
plt.plot(ra[w_haz2], dec[w_haz2], marker='o', ls='none')
plt.plot(ra[w_haz3], dec[w_haz3], marker='o', ls='none')
plt.plot(ra[w_haz4], dec[w_haz4], marker='o', ls='none')
plt.show()
plt.plot(et[w_haz0], marker='o', ls='none')
plt.plot(et[w_haz1], marker='o', ls='none')
plt.plot(et[w_haz2], marker='o', ls='none')
plt.plot(et[w_haz3], marker='o', ls='none')
plt.plot(et[w_haz4], marker='o', ls='none')
if (do_fft):
raise ValueError('Sorry, do_ffit not implemented')
return -1
if (do_sfit):
return (frame_med_sfit, file_base)
else:
return (frame_med, file_base)
# =============================================================================
# End of Function
# =============================================================================
if (__name__ == '__main__'):
stretch = astropy.visualization.PercentileInterval(90) # PI(90) scales array to 5th .. 95th %ile
print("Testing...")
index_group = 8
index_files = hbt.frange(0,47)
do_fft = False
power = 5
do_sfit = False
(arr,mask) = nh_create_straylight_median(index_group, index_files, do_fft=do_fft, do_sfit=do_sfit, power=power)
plt.set_cmap('plasma')
plt.imshow(stretch(hbt.remove_sfit(arr, degree=5)))
def plot(self, scale='log', percent = 98):
"""
Plot the grid. Do it in a good way, with labels, and with proper orientation.
Optional parameters
-----
scale:
The scaling method to use. Can be `log` or `linear`.
"""
origin = 'lower' # Set imshow() to start w/ (0,0) at lower-left
do_stretch_log = ('log' in scale)
# Define the axes. DK says that the array is delivered in order [x, y, z], which are same as Mark's coord frame.
# That means that if I sum in the '0' direction, I will have a plot in Y and Z.
axes = ['X', 'Y', 'Z']
num_axis = {'X' : 0, 'Y' : 1, 'Z' : 2}
# Now, make a dictionary to show us what the axes will be of the output image after doing np.sum().
# The dictionary here means:
# If we sum along the X axis (0), and we plot the result, what will be on vert axis of the imshow() plot.
# In this case, first remaining axis (Y) is on vertical, and second (Z) is on horizontal.
# That is how imshow() works.
axes_vertical = {'X':'Y', 'Y':'X', 'Z':'X'}
axes_horizontal= {'X':'Z', 'Y':'Z', 'Z':'Y'}
axes_transpose = {'X':True,'Y':True,'Z':True}
view = {'X':'Side', 'Y':'Front', 'Z':'Top'} # "If summed along Z axis, this is a Top view", etc.
# Set the font size
hbt.fontsize(10)
fontsize_axes = 15
width_colorbar = 10
halfwidth_km = self.km_per_cell_x * hbt.sizex(self.density) / 2
extent = [-halfwidth_km, halfwidth_km, -halfwidth_km, halfwidth_km] # Make calibrated labels for X and Y axes
i = 1 # Index of which plot we are on
for axis in axes:
plt.subplot(1,3,i)
# Plot the individual image. Start it with origin at lower-left corner.
img = np.sum(self.density, axis=num_axis[axis]) # Make the flattened image
if do_stretch_log:
img_stretch = stretch_hbt(img)
else:
img_stretch = astropy.visualization.PercentileInterval(percent)(img)
# Create the colorbar, and superimpose it on the image
colorbar = hbt.frange(np.amin(img_stretch), np.amax(img_stretch), hbt.sizey(img_stretch))
# Manually draw the colorbar onto the plot
if axes_transpose[axis]:
for j in range(width_colorbar):
img_stretch[-j,:] = colorbar # There is probably a better way to do this?
else:
for j in range(width_colorbar):
img_stretch[:,-j] = colorbar # There is probably a better way to do this?
# Display the image.
# The image is displayed in exactly the same orientation as if I print it, with the exception
# that the origin={lower | upper} keyword can flip it vertically.
# When accessing the array elements, they are in order img[y, x] -- which is opposite IDL.
if axes_transpose[axis]:
plt.imshow(np.transpose(img_stretch), extent=extent, origin=origin)
else:
plt.imshow( img_stretch, extent=extent, origin=origin)
# Create the labels for the colorbar, and individually place them
num_ticks_colorbar = 5 # Number of vertical value to put on our colorbar
for j in range(num_ticks_colorbar):
val = stretch_hbt_invert(hbt.frange(np.amin(img_stretch), np.amax(img_stretch), num_ticks_colorbar)[j])
val = round(val) # Convert to zero if it is very close
xval = 0.65*np.max(extent)
yrange = np.max(extent)-np.min(extent)
yval = np.min(extent) + 0.02*yrange + (j/(num_ticks_colorbar-1) * 0.92*yrange)
if do_stretch_log:
plt.text(xval, yval, f'{val:.1e}', color = 'white') # Label the colorbar, if log stretch only.
# Label the axes and the plot
if axes_transpose[axis]:
plt.title(f'Summed along {axis} ({view[axis]})', fontsize=fontsize_axes)
plt.xlabel(axes_vertical[axis] + ' [km]', fontsize=fontsize_axes)
plt.ylabel(axes_horizontal[axis] + ' [km]', fontsize=fontsize_axes)
plt.tight_layout()
else:
plt.title(f'Summed along {axis}', fontsize=fontsize_axes)
plt.ylabel(axes_vertical[axis] + ' [km]', fontsize=fontsize_axes)
plt.xlabel(axes_horizontal[axis] + ' [km]', fontsize=fontsize_axes)
plt.tight_layout()
i+=1
plt.show()
def test_scatter_mie_ensemble():
import hbt
import numpy as np
from scatter_mie_ensemble import scatter_mie_ensemble
pi = math.pi
# Set up the scattering properties
n_refract = 1.33
m_refract = -0.001
nm_refract = complex(n_refract,m_refract)
# Define the wavelength
alam = 500*u.nm
# Set up the size distribution
alam = 500 * u.nm
rmin = 0.01 * u.micron
rmax = 50 * u.micron
num_r = 50
pi = math.pi
# Define the exponent of the size distribution
q_1 = 5
q_2 = 5
r_break=0.5*u.micron
r = hbt.frange(rmin, rmax, num_r, log=True)*u.micron # Astropy bug? When I run frange(), it drops the units.
n = hbt.powerdist_broken(r, r_break, q_1, q_2) # Power law
n = r**(-5)
# r_min = 0.1
# r_max = 20
# num_r = 30
# q = 3.5
# r = hbt.frange(r_min, r_max, num_r, log=True)*u.micron
# n = r.value**-q
#
# Set up the angular distribution
num_ang = 91
ang_phase = hbt.frange(0, pi, num_ang)*u.rad # Phase angle.
# =============================================================================
# Call the function
# =============================================================================
(phase, p11_out, qsca) = scatter_mie_ensemble(nm_refract, n, r, ang_phase, alam, do_plot=True)
# Now make a plot pair. One plot with a phase curve, and one with an n(r) distribution.
plt.subplot(1,2,1)
plt.plot(ang_phase.to('deg'), phase)
plt.xlabel('Phase Angle [deg]')
plt.title('q = {}'.format((q_1, q_2)))
plt.yscale('log')
plt.subplot(1,2,2)
plt.plot(r.to('micron'), n * r**2)
plt.xlabel('Radius [micron]')
plt.ylabel('Number')
plt.yscale('log')
plt.title('n(r) * r^2, q={}'.format((q_1, q_2)))
plt.xscale('log')
plt.show()
lun.close()
# Process the group names. Some of this is duplicated logic -- depends on how we want to use it.
groups = astropy.table.unique(t, keys=(['Desc']))['Desc']
index_group = 7
index_images = [15, 16]
method = 'String'
vars = 'mask_7_8-15 p5'
# vars = '64-66 p10 *1.5 mask_7_61-63'
groupmask = (t['Desc'] == groups[index_group])
t_group = t[groupmask]
index_images_stray = hbt.frange(8, 15)
# Set up the stray light mask file (created w Photoshop)
file_mask_stray = '/Users/throop/Data/NH_Jring/masks/mask_{}_{}-{}.png'.format(
index_group, np.min(index_images_stray), np.max(index_images_stray))
dir_backplanes = '/Users/throop/data/NH_Jring/out/'
# Now loop over the images
for index_image in index_images:
file_image = t_group[index_image]['Filename']
# Load the object mask
data_df99 = ascii.read(file_df99)
data_hbt = ascii.read(file_hbt)
# Clip the data so that when we have N=1, the errorbars don't go to infinity
data_hbt['Error'] = np.clip(np.sqrt(data_hbt['Number']), 0.5, 1000)
data_hbt['Error'][0] = 0.7
data_hbt['Error'][1] = 0.7
# Make a distribution n(r)
q = np.array([2, 3, 4, 5, 5, 6])
numbins = 20
r = hbt.frange(0.001, 1000, numbins, log=True) # Go from small to big
#==============================================================================
# Make a plot showing my n(r) vs DF99
#==============================================================================
#n = r**(-q) # This is n(r) in the bin
#ngtr = n.copy()
#for i in range(numbins):
# ngtr[i] = np.sum(n[i:-1]) # Num > r: sum from here to big
DO_PLOT_ALL_Q = False
if (DO_PLOT_ALL_Q):
for q_i in q:
n = r**(-q_i)
t['groupnum'] = np.zeros(len(t)).astype(int)
t['imagenum'] = np.zeros(len(t)).astype(int)
# Standardize the reqid field, so it is sortable
t['ReqID_fixed'] = t['ReqID']
for i in range(len(t)):
t['ReqID_fixed'][i] = fix_reqid(t['ReqID'][i])
# Loop over all the groups, and assign a group and image number to each file
for groupnum,group in enumerate(groups_all):
is_match = t['Desc'] == group
t['groupnum'][is_match] = groupnum
t['imagenum'][is_match] = hbt.frange(0,np.sum(is_match)-1).astype(int)
# Now get a list of all reqid's
reqids_all = astropy.table.unique(t, keys=(['ReqID_fixed']))['ReqID']
# Now get a list of reqid's, for rings only!
groups_rings = groups_all[5:]
groupmask = np.logical_or( (t['Desc'] == groups_rings[0]),
(t['Desc'] == groups_rings[1]))
groupmask = np.logical_or(groupmask, t['Desc'] == groups_rings[2])
groupmask = np.logical_or(groupmask, t['Desc'] == groups_rings[3])
groupmask_rings = groupmask
t_rings = t[groupmask_rings]
im_clean = im.copy()
is_outlier = im > (np.median(im) + 3*std)
im_clean[is_outlier] = np.median(im)
# Do it again
std = np.std(im_clean)
im_clean2 = im_clean.copy()
is_outlier = im_clean > (np.median(im_clean) + 3*std)
im_clean2[is_outlier] = np.median(im_clean)
#==============================================================================
# Measure the radial profile, from Pluto
#==============================================================================
bins_radius = hbt.frange(np.amin(radius), np.amax(radius), nbins_radius) # Set up radial bins, in km
dradius = bins_radius[1] - bins_radius[0]
bin_number_2d = np.copy(im)*0
dn_mean_arr = np.zeros(nbins_radius)
dn_median_arr = np.zeros(nbins_radius)
dn_std_arr = np.zeros(nbins_radius)
npix_arr = np.zeros(nbins_radius)
dn_mean_clean_arr = np.zeros(nbins_radius)
dn_median_clean_arr = np.zeros(nbins_radius)
for i in range(nbins_radius-1):
is_good = np.array(radius > bins_radius[i]) \
def nh_jring_unwrap_ring_image(im,
num_bins_radius, limits_radius,
binsize_azimuth,
planes, dx=0, dy=0, mask_stray=None, mask_objects=None):
"""
Unwrap a 2D ring image from (RA, Dec) into (radius, azimuth).
Parameters:
-----
All of these parameters are mandatory.
im:
Image array
num_bins_radius:
Number of radial bins. **If this is too large, then we get a 'stretching' artifact**.
limits_radius:
Extent of the inner and outer radius, in km.
binsize_azimuth:
size of azimuthal bins, in radians.
planes:
The table of backplanes
mask_stray:
2D array of pixel flags. True = good.
mask_objects:
2D array of pixel flags. True = good.
dx, dy:
Pixel values to roll the image by -- that is, an additional offset to be added to nav info in WCS header.
Both the image and the mask are rolled by this amount. Integer.
Output
------
(im_unwrapped, bins_radius, bins_azimuth)
"""
import hbt
import numpy as np
from scipy.interpolate import griddata
import math
import matplotlib.pyplot as plt
# Process input
if (mask_objects is None): # NB: We need to use 'is' here. '==' will do an element-by-element comparison.
DO_MASK_OBJECTS = False # Alternatively, could also do 'if type(mask) is np.ndarray'
else:
DO_MASK_OBJECTS = True
if (mask_stray is None): # NB: We need to use 'is' here. '==' will do an element-by-element comparison.
DO_MASK_STRAY = False # Alternatively, could also do 'if type(mask) is np.ndarray'
else:
DO_MASK_STRAY = True
# https://stackoverflow.com/questions/36783921/check-if-variable-is-none-or-numpy-array-in-python
# https://stackoverflow.com/questions/15008380/double-equals-vs-is-in-python
# DO_MASK = (mask != None) # If we are passed the 'mask' value, then
# Extract fields from the backplane array
radius = planes['Radius_eq'] # These are properly 4x4 or 1x1, as desired.
azimuth = planes['Longitude_eq']
phase = planes['Phase']
#==============================================================================
# Examine backplane to figure out azimuthal limits of the ring image
#==============================================================================
bins_radius = hbt.frange(limits_radius[0], limits_radius[1], num_bins_radius)
# Select the ring points -- that is, everything inside the mask
is_ring_all = ( np.array(radius > limits_radius[0]) & np.array(radius < limits_radius[1]))
# Make sure there are some valid data points. If not, return an error
if (np.sum(is_ring_all) == 0):
print("Error: No valid ring points between radius {:,.0f} .. {:,.0f} km".format(limits_radius[0],
limits_radius[1]))
print("Image radius limits = {:,.0f} .. {:,.0f} km".format(np.amin(radius), np.amax(radius)))
raise ValueError('NoValidRingPoints')
radius_all = radius[is_ring_all] # Make a list of all of the radius values
azimuth_all = azimuth[is_ring_all] # Make a list of all of the azimuth points for all pixels
phase_all = phase[is_ring_all]
dn_all = np.roll(np.roll(im, int(round(dy)), 0), int(round(dx)), 1)[is_ring_all]
# Axis 0 is y. 1 is x.
# If a float is passed, round to the closest int
# phase_mean = np.mean(phase_all) # Get the mean phase angle across the ring.
#
# Now take these raw data, and rearrange them so that we can take the longest continuous segment
# We do this by appending the timeseries to itself, looking for the largest gap (of no az data),
# and then the data will start immediately after that.
# _2 indicates a double-length array (ie, with [azimuth, azimuth + 2pi])
# _s indicates sorted
# _d indicates delta
azimuth_all_3 = np.concatenate((azimuth_all, azimuth_all + 2*math.pi, azimuth_all + 4*math.pi))
dn_all_3 = np.concatenate((dn_all, dn_all, dn_all))
radius_all_3 = np.concatenate((radius_all, radius_all, radius_all))
azimuth_all_3_s = np.sort(azimuth_all_3, kind = 'heapsort')
azimuth_all_3_s_d = azimuth_all_3_s - np.roll(azimuth_all_3_s, 1)
# Look for the indices where the largest gaps (in azimuth) start
# XXX we get an error here on images if there are no valid ring points.
index_seg_start_3_s = (np.where(azimuth_all_3_s_d > 0.999* np.max(azimuth_all_3_s_d)))[0][0]
index_seg_end_3_s = (np.where(azimuth_all_3_s_d > 0.999* np.max(azimuth_all_3_s_d)))[0][1]-1
# Get proper azimithal limits. We want them to be a single clump of monotonic points.
# Initial point is in [0, 2pi) and values increase from there.
azimuth_seg_start = azimuth_all_3_s[index_seg_start_3_s] # Azimuth value at the segment start
azimuth_seg_end = azimuth_all_3_s[index_seg_end_3_s] # Azimuth value at the segment end
# Quantize these values to the next-lower and next-upper bins (e.g., 0.001543 → 0.001), to use a common base.
azimuth_seg_start = azimuth_seg_start - np.mod(azimuth_seg_start, binsize_azimuth) - binsize_azimuth
azimuth_seg_end = azimuth_seg_end - np.mod(azimuth_seg_end, binsize_azimuth) + binsize_azimuth
# Calculate number of bins
# NB: Must use round() not int() here to avoid 15.999999 → 15. And then int for benefit of numpy.
num_bins_azimuth = int( round( (azimuth_seg_end - azimuth_seg_start) / binsize_azimuth) + 1 )
indices_3_good = (azimuth_all_3 >= azimuth_seg_start) & (azimuth_all_3 < azimuth_seg_end)
azimuth_all_good = azimuth_all_3[indices_3_good]
radius_all_good = radius_all_3[indices_3_good]
dn_all_good = dn_all_3[indices_3_good]
# Extract arrays with the proper pixel values, and proper azimuthal values
azimuth_all = azimuth_all_good
radius_all = radius_all_good
dn_all = dn_all_good
if (DO_MASK_OBJECTS):
mask_objects_roll = np.roll(np.roll(mask_objects, int(round(dy)), 0), int(round(dx)), 1)
mask_objects_all = mask_objects_roll[is_ring_all]
mask_objects_all_3 = np.concatenate((mask_objects_all, mask_objects_all, mask_objects_all))
mask_objects_all_good = mask_objects_all_3[indices_3_good]
mask_objects_all = mask_objects_all_good
if (DO_MASK_STRAY):
mask_stray_roll = np.roll(np.roll(mask_stray, int(round(dy)), 0), int(round(dx)), 1)
mask_stray_all = mask_stray_roll[is_ring_all]
mask_stray_all_3 = np.concatenate((mask_stray_all, mask_stray_all, mask_stray_all))
mask_stray_all_good = mask_stray_all_3[indices_3_good]
mask_stray_all = mask_stray_all_good
#==============================================================================
# Now regrid the data from xy position, to an unrolled map in (azimuth, radius)
#==============================================================================
# Construct the gridded image line-by-line
dn_grid = np.zeros((num_bins_radius, num_bins_azimuth)) # Row, column
bins_azimuth = hbt.frange(azimuth_seg_start, azimuth_seg_end, num_bins_azimuth)
bins_radius = hbt.frange(limits_radius[0], limits_radius[1], num_bins_radius)
if (DO_MASK_OBJECTS):
mask_objects_grid = dn_grid.copy()
if (DO_MASK_STRAY):
mask_stray_grid = dn_grid.copy()
for i in range(num_bins_radius-1): # Loop over radius -- inner to outer. Do one radial output bin at a time.
# Select only bins with right radius and azimuth
is_ring_i = np.array(radius_all > bins_radius[i]) & np.array(radius_all < bins_radius[i+1]) & \
np.array(azimuth_all > azimuth_seg_start) & np.array(azimuth_all < azimuth_seg_end)
if np.sum(is_ring_i) > 0:
dn_i = dn_all[is_ring_i] # Get the DN values from the image (adjusted by nav pos error)
radius_i = radius_all[is_ring_i]
azimuth_i = azimuth_all[is_ring_i]
# Now make sure there is not a large gap in azimuth in the data. If there is, then make it out w/ NaN's.
# This happens when the ring ansae gets near the image edge. griddata() will blindly interpolate,
# but we want to fill gap w/ NaN so that it will not do so.
do_plug_gaps = True
if do_plug_gaps:
# Put the azimuth points in monotonic order. They are not otherwise (and griddata does not require).
# But, to look for gaps, we need to sort
d_azimuth_gap_max = 0.05 # Max width of a gap, in radians. Larger than this will be NaN-plugged.
indices = np.argsort(azimuth_i)
azimuth_i_sort = azimuth_i[indices]
dn_i_sort = dn_i[indices]
# Check the point-by-point increase in azimuth
d_azimuth_i_sort = azimuth_i_sort - np.roll(azimuth_i_sort,1)
# Flag it if it exceeds some pre-set size
is_gap = np.abs(d_azimuth_i_sort) > d_azimuth_gap_max
# And then put NaNs at the start and end of the gap
is_gap[0] = False
if np.sum(np.where(is_gap)):
w = np.where(is_gap)[0][0]
dn_i_sort[w-1:w+2] = np.nan
grid_lin_i = griddata(azimuth_i_sort, dn_i_sort, bins_azimuth, method='linear')
dn_grid[i,:] = grid_lin_i # Write a row of the output array
# Now do the interpolation. If there are NaNs it will skip that region.
else:
grid_lin_i = griddata(azimuth_i, dn_i, bins_azimuth, method='linear')
dn_grid[i,:] = grid_lin_i # Write a row of the output array
if DO_MASK_STRAY:
mask_stray_i = mask_stray_all[is_ring_i] # Get the DN values from the image
# (adj by nav pos error)
grid_lin_i = griddata(azimuth_i, mask_stray_i, bins_azimuth, method='linear')
mask_stray_grid[i,:] = grid_lin_i
if DO_MASK_OBJECTS:
mask_objects_i = mask_objects_all[is_ring_i]
grid_lin_i = griddata(azimuth_i, mask_objects_i, bins_azimuth, method='linear')
mask_objects_grid[i,:] = grid_lin_i
# The way I've done the regridding, each output bin goes from n:n+1. So, the final bin is empty. Just duplicate it.
# There is probably a better way to do this.
# This kind of means that my output array is shifted 1/2-bin from my input array. Ugh.
# Also, this routine is quite slow, and I really think it introduces some artifacts. If I was a CS major,
# I could write a much better version of this algorithm.
#
# Algorithm uses griddata(), which is just interpolation. So, while it does not preserve 'area*flux', it does preserve
# the actual DN values ('DN per pixel') -- and it creates new pixels, with the same DN-per-pixel values.
# So, a radial profile, or azimuthal profile, by taking the mean along one axis, should work as intended, and give
# a value in DN-per-pixel.
n = num_bins_radius
dn_grid[n-1,:] = dn_grid[n-2,:]
mask_stray_grid[n-1,:] = mask_stray_grid[n-2,:]
mask_objects_grid[n-1,:] = mask_objects_grid[n-2,:]
# Save the variables, and return
image_unwrapped = dn_grid # NB: This has a lot of NaNs in it.
if (DO_MASK_OBJECTS and DO_MASK_STRAY):
mask_stray_unwrapped = mask_stray_grid
mask_objects_unwrapped = mask_objects_grid
# Convert these to booleans, and set any NaN to be False (since they are probably off-edge)
return (image_unwrapped, mask_stray_unwrapped, mask_objects_unwrapped, bins_radius, bins_azimuth)
else:
return (image_unwrapped, bins_radius, bins_azimuth)
if IS_4X4:
ang_pix = ang_fov / 256 # Radians per pixe, 4X4
else:
ang_pix = ang_fov / 1024 # Radians per pixel, 1X1
ang_deadband = ang_deadband_deg * hbt.d2r # Deadband size
drift_per_sec_pix = rate_drift / ang_pix
num_sum = num_steps # corect?? XXX I had to add this line; not sure if it is right or not.
dt = length_sec / num_sum # Timestep
t = hbt.frange(0, length_sec, num_sum)
# Need to make a function which
ang_x = np.zeros(num_steps) # Angle, in radians, at each timestep
ang_y = np.zeros(num_steps)
ang_rate_x = np.zeros(num_steps) # Drift rate, in radians/second, at each timestep
ang_rate_y = np.zeros(num_steps)
# Set the position and drift rate at initial timestep
ang_x[0] = 0
ang_y[0] = 0
ang_rate_x[:] = ang_rate_nominal
ang_rate_y[:] = ang_rate_nominal/2
et_end = et_start + 30*minute
radius_image = 2500*u.km
radius_kbo = 20*u.km
radius_ring = 1000*u.km
radius_ring_km = radius_ring.to('km').value
radius_ring_km = np.array([150, 500, 1250])
#==============================================================================
# Set up the times for each exposure
#==============================================================================
n_exp = n_footprints * exp_per_footprint # Total number of exposures
index_exp = hbt.frange(0,n_exp-1)
index_footprint = np.trunc(index_exp/3).astype('int')
# Define 'et' as an array, one per exposure, of the time that exposure is taken
et = et_start + (index_exp * exptime) + (index_footprint * dt_slew)
dist_kbo = np.zeros(n_exp)
for i,et_i in enumerate(et):
(st, junk) = sp.spkezr(name_target, et_i, 'J2000', 'LT+S', name_observer)
dist_kbo[i] = sp.vnorm(st[0:2])
dist_kbo = dist_kbo * u.km
width_fov_km = (dist_kbo * width_fov_rad).to('km').value # Width, in km
plt.set_cmap('plasma')
rj_km = 71492
# List all of the Gossamer observations. I have determined these groupings manually, based on timings.
# In general it looks like usually these are stacks of four frames at each pointing ('footprint')
# Lauer's footprints are just numbered sequentially (f01, f02, etc). So, we need to keep these files here in
# same order, so as to correlate exactly w/ Lauer's.
index_group = 6
index_image_list = [
np.array([54]), # 1X1. Main ring. 1.6 .. 1.9 RJ. Right ansa. One image, edge-on.
hbt.frange(59,62), # Right ansa. -2.7 RJ. Gossamer maybe there but hidden -- need to optimize.
hbt.frange(63,66), # Left ansa. Furthest out, no ring. Use for subtraction.
hbt.frange(67,70), # Left ansa. Far out, no ring. Closer than above.
hbt.frange(71,74), # Left ansa. No ring. Closer than above.
hbt.frange(75,78), # Left ansa. Gossamer. Closer than above.
# np.array([81]), # Left ansa. Main ring. Prob gossamer too but not interested. 1X1. Svrl ptgs.
hbt.frange(95,98), # Right ansa. Gossamer limb.
hbt.frange(99,102), # Left ansa. Similar geometry as 75-78.
hbt.frange(112,115),# Right ansa. Gossamer limb. Similar geometry as 95-98 (offset pointing)
hbt.frange(116,119),# Left ansa. Similar geometry as 75-78. Sat visible??
hbt.frange(120,123), # Left ansa. Closer than above.
hbt.frange(124,127), # Left ansa. Closer than above.
hbt.frange(128,131), # Left ansa + main ring ansa. Closer than above.
# hbt.frange(132,135), # Main ring. Left side, well inside of gossamer.
hbt.frange(157,160),
import numpy as np
import hbt
# Make an array of images on a PDF file.
# Based on http://stackoverflow.com/questions/2252726/how-to-create-pdf-files-in-python , near the end.
pp = PdfPages("out.pdf")
fs = 5
i = 1 # Current image #
num_rows = 2
num_cols = 2
im = hbt.dist_center(1001)
for row in hbt.frange(1,num_rows, num_rows):
for col in hbt.frange(1, num_cols, num_cols):
p = plt.subplot(num_rows, num_cols,i) # Image 1
plt.imshow(im)
a = plt.gca()
a.get_xaxis().set_visible(False) # We don't need axis ticks
a.get_yaxis().set_visible(False)
# plotImage(files[1])
str = '{:d}, X={:d}, Y={:d}'.format(int(i), int(col), int(row))
plt.text(0, -20, str, fontsize = fs)
plt.text(0, -60, str, fontsize = fs)
if (i == 1):
# Create the plot q = np.array([1.5, 2, 2.5, 3, 3.5, 4, 5, 6, 7]) # 9 elements long q = np.array([2, 3.5, 5]) # 4 elements long #p = plot([3,4], xtitle = 'Radius [$\mu$m]' ,$ # ytitle = 'Total number N > r impacting NH during encounter',xrange=[0.1,1000d],yrange=yrange, # /XLOG, /YLOG, /NODATA, $ # title = title) #p_arr = replicate(p, sizex(q)) # Draw a dotted line at the two danger sizes that SAS specified at 3-Nov-2011 workshop r = hbt.frange(rmin, rmax, num_r, log=True)*u.micron # Astropy bug? When I run frange(), it drops the units. qmie = np.zeros(num_r) qsca = np.zeros(num_r) qext = np.zeros(num_r) qbak = np.zeros(num_r) qabs = np.zeros(num_r) p11_mie = np.zeros(num_r) bin_r_danger_1 = np.where(r > r_danger_1)[0][0] # Calculate the transition regime binstart_trans = hbt.wheremin(np.abs(r - r_trans/halfwidth_trans)) binend_trans = hbt.wheremin(np.abs(r - r_trans*halfwidth_trans))
def nh_create_straylight_medians():
"""
This is a wrapper routine which calls the main function. It is just for testing.
"""
plt.rc('image', cmap='Greys_r')
segment = 4 # 1, 2, or 3
dir_out = '/Users/throop/data/NH_Jring/out/'
fs = 15 # Set the font size
if (segment == 1): # 50 frames, upright
frames_med = np.array([1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19])
frames_med = np.array([1,2,3,4,5])
index_files = frames_med
index_group = 8
# num_frames_med = np.size(frames_med)
frames_data = hbt.frange(0,48,49) # 0 .. 49
if (segment == 2): # 5 frames, tilted sideways
frames_med = np.array([49,51,52,53,53])
num_frames_med = np.size(frames_med)
frames_data = frames_med
if (segment == 3): # 5 frames, tilted sideways
frames_med = hbt.frange(54,111,58)
num_frames_med = np.size(frames_med)
frames_data = frames_med
# Get the straylight frame
im = nh_create_straylight_median(index_group, index_files, do_fft=False, do_sfit=True, power1=5, power2=5)
# Save the straylight frame itself
outfile = dir_out + 'embedded_seg' + repr(int(segment)) + '_med' + repr(int(num_frames_med)) + '_sfit.png'
matplotlib.image.imsave(outfile, frame_sfit_med)
print 'Wrote: ' + outfile
outfile = dir_out + 'embedded_seg' + repr(int(segment)) + '_med' + repr(int(num_frames_med)) + '_ffit.png'
matplotlib.image.imsave(outfile, frame_ffit_med)
print 'Wrote: ' + outfile
file_out = 'med_g9_n0-49_sfit8_571_ps.pkl'
#for i,n in enumerate(frames_data):
#for i in range(5):
outfile = dir_out + 'embedded_seg' + repr(int(segment)) + '_med' + repr(int(num_frames_med)) + \
'_frame' + repr(int(i)) + '.png'
file = t_group['Filename'][n] # Look up filename
print file
print "Writing: " + outfile
frame = hbt.read_lorri(file,frac_clip = 1)
im = hbt.remove_brightest(frame - frame_sfit_med, 0.97, symmetric=True)
im2 = hbt.remove_brightest(im - hbt.sfit(im,power2), 0.97, symmetric=True)
arr_x = eval('np.' + t_group['x_pos_ring2'][n]) # Ring2 = outer ring
arr_y = eval('np.' + t_group['y_pos_ring2'][n])
ymean = np.mean(arr_y)
xmean = np.mean(arr_x)
ymin = np.min(arr_y) # top of screen -- for upward pointing ansae
ymax = np.max(arr_y) # Bottom of screen -- for downward pointing ansae
xmin = np.min(arr_x) # Left edge
xmax = np.max(arr_x) # Right edge
if (segment == 1): #
roll_x = -int(xmin - 100) # Roll to __ from left edge
roll_y = -int(ymin - 200) # Roll to __ from top edge
if (segment == 2):
roll_x = -int(xmean - 400)+500
roll_y = -int(ymean - 3900)-1050
if (segment == 3):
roll_x = -int(xmean - 400)+100
roll_y = -int(ymean - 2600) # -3200 is toward top. -3400 is toward bottom
# Now read all the frames, and process them one by one.
# Output as images which can be animated.
## *** Need to roll the image properly as per navigation!
pad_dx = 400 # Amount to add in x dir, total
pad_dy = 400
im_pad = np.zeros((1024 + pad_dx, 1024 + pad_dy))-20
im_pad[pad_dx/2:-pad_dx/2, pad_dy/2:-pad_dy/2] = im2
im_roll = np.roll(np.roll(im_pad, roll_x, axis=1), roll_y, axis=0)
ax = plt.imshow(im_roll, vmin=-20, vmax=20)
plt.title(repr(i) + ', ' + t_group['Shortname'][n])
plt.axis('off')
#+ ', xmean=' + repr(int(xmean)) +
# ', ymean=' + repr(int(ymean)), fontsize=fs)
# Save the image
matplotlib.image.imsave(outfile, im_roll)
plt.show()
plt.subplot(1,2,1) # Reversed! num cols, num rows ** Good reduction. Largest az etent.
plt.imshow(frame_sfit_med)
plt.title('frame_sfit_med, n=' + repr(num_frames_med))
#plt.show()
plt.subplot(1,2,2) # Reversed! num cols, num rows ** Good reduction. Largest az etent.
plt.imshow(frame_ffit_med)
plt.title('frame_ffit_med, n=' + repr(num_frames_med))
plt.show()
def get_radial_profile_backplane(im, radius_plane, method='median', num_pts = 100, do_std=False):
"""
Extract a radial profile from an image.
Uses a backplane passed in.
Parameters
-----
im:
Array of data values (e.g., the image).
radius_plane:
2D array, which is the backplane. Typically this is planes['Radius_eq'].
num_pts:
Scalar. Number of points to use in the output array. Output radius is evenly spaced
from 0 .. max(radius_plane).
Optional parameters
-----
method:
String. 'mean' or 'median'.
do_stdev:
Boolean. If set, compute the standard deviation, and return in the tuple
"""
radius_1d = hbt.frange(0, int(np.amax(radius_plane)), num_pts)
profile_1d = 0. * radius_1d.copy()
std_1d = profile_1d.copy()
for i in range(len(profile_1d)-2):
# Identify the pixels which are at the right distance
is_good = np.logical_and(radius_plane >= radius_1d[i],
radius_plane <= radius_1d[i+1])
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=RuntimeWarning)
if (method == 'mean'):
profile_1d[i] = hbt.nanmean(im[is_good])
if (method == 'median'):
profile_1d[i] = hbt.nanmedian(im[is_good])
# clipped = astropy.stats.sigma_clip(im[is_good], sigma=1.5)
# std_1d[i] = np.nanstd(clipped)
if do_std:
return (radius_1d, profile_1d, std_1d)
return (radius_1d, profile_1d)
if __name__ == '__main__':
import astropy.visualization
stretch_percent = 90
stretch = astropy.visualization.PercentileInterval(stretch_percent) # PI(90) scales to 5th..95th %ile.
arr = hbt.nh_get_straylight_median(6,[120,121,122,123,124],do_sfit=True, power=5)
plt.imshow(stretch(arr))
arr = hbt.nh_get_straylight_median(6,[120,121,122,123,124],do_sfit=True, power=10)
plt.imshow(stretch(arr))
arr = hbt.nh_get_straylight_median(6,[120,121,122,123,124],do_sfit=False, power=2)
plt.imshow(arr)
arr = hbt.nh_get_straylight_median(6,[120,121,122,123,124],do_sfit=True, power=5)
plt.imshow(arr)
arr_bg = hbt.nh_get_straylight_median(7,[49,50,51],do_sfit=False)
arr_image = hbt.nh_get_straylight_median(7,[52], do_sfit=False)
plt.imshow(stretch(hbt.remove_sfit(arr_image - arr_bg,degree=1)))
# Now try one for real, from 8/0-48 sequence.
# There are a lot of ring artifacts left we wnt to get rid of.
arr = hbt.nh_get_straylight_median(8,hbt.frange(0,48), do_sfit=True, power=5)
plt.imshow(stretch(hbt.remove_sfit(arr,degree=1)))
#==============================================================================
# Cross-correlate these signals and shift them radially in order to align them using radial profiles
#==============================================================================
limit_shift = np.array([127000,130000])
limit_shift_bin = hbt.x2bin(limit_shift, radius[0,:])
shift = np.zeros((numfiles)).astype(int)
profile_radius_dn_roll = profile_radius_dn.copy()
dx_max = 20 # look at all the posible shifts, from -dx_max to +dx_max, which is 2*dx_max+1 different integers
correl = np.zeros((numfiles, dx_max*2 + 1))
for i in range(numfiles):
for j,dx in enumerate(hbt.frange(-dx_max, dx_max).astype(int)):
correl[i,j] = np.correlate(profile_radius_dn[0,limit_shift_bin[0]:limit_shift_bin[1]], \
np.roll(profile_radius_dn[i,limit_shift_bin[0]:limit_shift_bin[1]],dx))
if np.isnan(correl[i,j]): # Some of the radial profiles have nans in them. For these, just skip the correlation
correl[i,j] = 1
shift[i] = (hbt.wheremax(correl[i,:])) - dx_max
profile_radius_dn_roll[i,:] = np.roll(profile_radius_dn[i,:],shift[i])
# Shift each image vertically
for i in range(numfiles):
bin_inner_vnorm = hbt.x2bin(131000, radius[i,:])
bin_outer_vnorm = hbt.x2bin(133000, radius[i,:])
profile_radius_dn_roll[i,:] -= np.mean(profile_radius_dn_roll[i,bin_inner_vnorm:bin_outer_vnorm])
d_target_summed = np.zeros((5,541))
d_summed = np.zeros((32,1024))
for i,file in enumerate(file_list):
hdulist = fits.open(file)
d = hdulist['PRIMARY'].data # Units of this are float, but I'm not sure what they are. I would prefer raw counts.
d_target = d[13:18, 370:911] # Keep in mind that 13:18 really means 13:17...
d_target_summed += d_target
d_summed += d
p = hdulist['PIXEL_LIST_TABLE'].data
count_rate_fits_i = hdulist['COUNT_RATE'].data
num_samples = hdulist['COUNT_RATE'].header['NAXIS1'] # Number of samples in this file
dt = hdulist['COUNT_RATE'].header['SAMPLINT'] # Count rate sampling interval [sec]
bins = hbt.frange(0, num_samples) # Get a list of all of the timestep bins, inclusive, for this file.
# Use '+1' so we create the histogram upper size bin.
# Now downselect the pixel list for just the photons in the proper X and Y position on the detector
is_good = (p['Y_INDEX'] < 18) & (p['Y_INDEX'] >= 15) & (p['X_INDEX'] >= 370) & (p['X_INDEX'] < 910)
# Now we have a list of all of the good pixels. For each of these, now we want to grab its timestep.
timesteps_good = p['TIMESTEP'][is_good]
timesteps_all = p['TIMESTEP']
# Now count how many photons are in each timestep bin. I have defined those timestep bins up above.
(count_rate_target_i, junk) = np.histogram(timesteps_good, bins)
(count_rate_i, junk) = np.histogram(timesteps_all, bins)
data_df99 = ascii.read(file_df99)
data_hbt = ascii.read(file_hbt)
# Clip the data so that when we have N=1, the errorbars don't go to infinity
data_hbt['Error'] = np.clip(np.sqrt(data_hbt['Number']), 0.5, 1000)
data_hbt['Error'][0] = 0.7
data_hbt['Error'][1] = 0.7
# Make a distribution n(r)
q = np.array([2, 3, 4, 5, 5, 6])
numbins = 20
r = hbt.frange(0.001, 1000, numbins, log=True) # Go from small to big
#==============================================================================
# Make a plot showing my n(r) vs DF99
#==============================================================================
#n = r**(-q) # This is n(r) in the bin
#ngtr = n.copy()
#for i in range(numbins):
# ngtr[i] = np.sum(n[i:-1]) # Num > r: sum from here to big
DO_PLOT_ALL_Q = False
if (DO_PLOT_ALL_Q):
for q_i in q:
n = r**(-q_i)
def get_radial_profile_backplane_quadrant(im, radius_plane, longitude_plane, method='median', num_pts = 100, do_std=False):
"""
Extract a radial profile from an image.
Uses a backplane passed in.
Returns four values, corresponding to the four quadrants.
Parameters
-----
im:
Array of data values (e.g., the image).
radius_plane:
2D array, which is the backplane. Typically this is planes['Radius_eq'].
num_pts:
Scalar. Number of points to use in the output array. Output radius is evenly spaced
from 0 .. max(radius_plane).
Optional parameters
-----
method:
String. 'mean' or 'median'.
do_stdev:
Boolean. If set, compute the standard deviation, and return in the tuple
"""
radius_1d = hbt.frange(0, int(np.amax(radius_plane)), num_pts)
profile_1d = np.zeros((4, len(radius_1d)))
std_1d = profile_1d.copy()
quadrant_plane = np.ceil((np.pi + longitude_plane) * 4 / (np.pi * 2)).astype(int) - 1 # Range = 0 .. 3
for i in range(len(radius_1d)-2):
for j in range(4):
# Identify the pixels which are at the right distance
is_good = np.logical_and(np.logical_and(radius_plane >= radius_1d[i],
radius_plane <= radius_1d[i+1],),
quadrant_plane == j)
# print(f'Summing {np.sum(is_good)} cells')
if (method == 'mean'):
profile_1d[j,i] = hbt.nanmean(im[is_good])
if (method == 'median'):
profile_1d[j,i] = hbt.nanmedian(im[is_good])
# clipped = astropy.stats.sigma_clip(im[is_good], sigma=1.5)
# std_1d[j,i] = np.nanstd(clipped)
if do_std:
return (radius_1d, profile_1d, std_1d)
return (radius_1d, profile_1d)
Created on Wed Mar 22 13:22:54 2017 @author: throop """ import numpy as np import matplotlib.pyplot as plt import hbt import astropy.units as u #%% hbt.figsize((4,5)) x = hbt.frange(0, 10,100) y = np.sin(x) fig, ax = plt.subplots() xval = 50000*u.km # Bug: clipping is not applied properly here! # The xval is converted to a .value when plotted, as expcted. # But if it has a unit with it, then the clip_on keyword is ignored. # This causes the plot to be huge, and (I guess) never appears on the screen. ### #set_clip_on(b) #Set whether artist uses clipping. #